Format of Locus File

The following description is adapted from Linkage and Tlinkage User Guides.

Default Name:  "datafile.dat"

This file describes the loci and different parameters necessary for the analyzing programs.

line 1:
Contains information on the following parameters: no. of loci (No_Loci), a risk locus (Risk_Locus),  if the data is sex linked or autosomal (Sex_Linked), Program Code (Program_Code) and no. of complex affection loci (No_Complex_Affection_Loci).

The format  is:    No_Loci    Risk_Locus    Sex_Linked    Program_Code    No_Complex_Affection_Loci
Valid values for the variables:
Example: 4 0 1 4 2  encodes for an analysis of 4 sex-linked loci, including two disease loci, using program SuperLinkmap.  16 0 0 5 0  encodes for an analysis of 16 autosomal loci, with one disease locus, using program SuperMlink.

line 2:
Contains information on the following parameters: a mutation locus (Mutation_Locus) and mutation rates (Mutation_Male & Mutation_Female), Haplotype frequencies (Hap_Freq, if 1).  This information is ignored by Superlink.

The format  is:      Mutation_Locus    Mutation_Male    Mutation_Female    Hap_Freq
Example: 0 0 0 0  or any other four numbers should constitute the second line.  These numbers are ignored.  We left this line to be consistent with Linkage/Fastlink input format.

line 3:
The chromosome order of the loci (the physical order assumed for the loci).

Example: 4 1 2 3 encodes the fact that the fourth locus (in the input order) is first on the map, the first  locus (in the input order) is second on the map, the second locus (in the input order) is third on the map, and the third locus (in the input order) is last on the map.

Starting at the fourth line, there is a description of each locus.  The loci are described in the order in which they appear in the pedigree file (input order, not map order).
The description differs according to the type of locus.

P(h)    P(d)
The third line consists of the number of liability classes (penetrance classes).
The next few lines consist of the penetrances for each genotype in each liability class.  For each liability class, the penetrances appear in a separate line, as follows:

    From version 1.4

For all loci type you can specify locus name. To do this, you need to write locus name between two '#' symbols after the number of the alleles. The program uses the name in the output tables.

 3     5   #locus5# << numbered alleles code, total number of alleles, locus name


The next two-three lines of the locus file provide recombination information.

        The following sex-difference options are possible: Example  A:
0  0  <<   no sex differenceno interference
0.1   0.3   0.2   0.1 <<   recombination fractions for a five-loci analysis

Example  B:
0  2  <<  no sex difference, 2 encodes interference with Kosambi's mapping function
0.1    0.3 <<  recombination fractions for a three-loci analysis

Example  C:
1  0  <<   1 encodes constant sex difference,  no interference
0.1    0.3 <<   male recombination fractions for a three-loci analysis
<<   female/male ratio of genetic distance

Example  D:
2  0  <<   2  encodes variable sex difference,   no interference
0.1    0.3  <<   male recombination fractions for a three-loci analysi
0.2    0.35 <<   female recombination fractions for a three-loci analysis

Example  E:
0  1  <<  no sex difference,  1 encodes interference without a mapping function
0.1    0.3    0.32  <<  theta(AB),   theta(BC),   theta(AC)

The locus file ends with one or several input lines describing program-specific information which consists of parameters that control the starting point(s), ending point(s), increment size(s), or number of evaluations requested, depending on the program code specified in line 1 of the locus file. The input line(s) are as follows. Explanations regarding these seven programs and their input lines are given in Program Options.

SuperLinkmap (program code 4): locus_varied    finishing_value    number_of_evaluations

SuperMlink (program code 5) :  recombination_varied     increment     finishing_value

SuperGH (program code 8):

                        <-s  step_iter   or  -n  num_iter>      start_pos        end_pos    <-o  off_end>
                        <-s  step_iter_1   or   -n  num_iter_1>     start_pos_1        end_pos_1        <-o  off_end_1>
                        <-s  step_iter_2   or   -n  num_iter_2>     start_pos_2        end_pos_2        <-o  off_end_2>

SuperBinaryIlink (program code 9):   locus_varied

SuperHaplo program (program code 10): no additional input is needed.

SuperOptLink program (program code 12):

    1    <-M>
    start_pos        end_pos        <-o    off_map>
SuperOptMarginal program (program code 13):

                    start_pos        end_pos        <-o    off_map>

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